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Conformers: ABBIImiBZICOPNSYNN
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Molecular Recognition of RNA by Neomycin and a Restricted Neomycin Derivative

Results of the assignment of 54 detected steps in 1 model(s), can be also downloaded as csv or json file. Average confal 0, percentile 0.

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Click a row in table or a step in viewer for analysis of results. Click column headers to sort data.
Define restraints for steps within Å cartesian RMSD, global sigma scaling factor or use per step sigma scaling.
step numberStep nameCANANtCconfalrmsd
011zz5_A_G2_U3AAwAA01600.27 AA01
021zz5_A_U3_G4AAwAA06700.38 AA06
031zz5_A_G4_G5AAwAA11830.31 AA11
041zz5_A_G5_U6AAAAA08690.33 AA08
051zz5_A_U6_G7AAAAA00950.14 AA00
061zz5_A_G7_A8NANNANT01.00 OP13
071zz5_A_A8_A9AAAAA00520.37 AA00
081zz5_A_A9_G10NANNANT00.74 OP30
091zz5_A_G10_U11AAuAA12610.49 AA12
101zz5_A_U11_C12AAAAA08860.19 AA08
111zz5_A_C12_G13AAwAA01600.21 AA01
121zz5_A_G13_C14NANNANT00.40 AA03
131zz5_A_C14_G15AAwAA01550.26 AA01
141zz5_A_G15_G16AAAAA00360.31 AA00
151zz5_B_C21_G22AAAAA00940.14 AA00
161zz5_B_G22_C23AAAAA00500.23 AA00
171zz5_B_C23_G24AAAAA00780.17 AA00
181zz5_B_G24_U25AAAAA00830.23 AA00
191zz5_B_U25_C26AAAAA00910.28 AA00
201zz5_B_C26_A27AAAAA00860.19 AA00
211zz5_B_A27_C28AAAAA00730.15 AA00
221zz5_B_C28_A29AAAAA00670.24 AA00
231zz5_B_A29_C30AAAAA00770.17 AA00
241zz5_B_C30_C31AAAAA00940.14 AA00
251zz5_B_C31_A32AAAAA00790.20 AA00
261zz5_B_A32_C33AAwAA01660.30 AA01
271zz5_B_C33_C34AAuAA12450.41 AA12
281zz5_C_G2_U3AAAAA00420.29 AA00
291zz5_C_U3_G4AAAAA00660.23 AA00
301zz5_C_G4_G5AAwAA01870.15 AA01
311zz5_C_G5_U6AAAAA08890.22 AA08
321zz5_C_U6_G7AAAAA00900.14 AA00
331zz5_C_G7_A8NANNANT01.09 OP13
341zz5_C_A8_A9AAAAA00120.41 AA00
351zz5_C_A9_G10NANNANT00.99 OP11
361zz5_C_G10_U11AAAAA08160.48 AA08
371zz5_C_U11_C12AAwAA06900.23 AA06
381zz5_C_C12_G13AAAAA00550.31 AA00
391zz5_C_G13_C14AAAAA00540.24 AA00
401zz5_C_C14_G15AAAAA00630.28 AA00
411zz5_C_G15_G16AAAAA00690.26 AA00
421zz5_D_C21_G22AAAAA00620.22 AA00
431zz5_D_G22_C23AAAAA00510.20 AA00
441zz5_D_C23_G24AAAAA00790.18 AA00
451zz5_D_G24_U25AAAAA00590.31 AA00
461zz5_D_U25_C26AAAAA00680.23 AA00
471zz5_D_C26_A27AAAAA00520.31 AA00
481zz5_D_A27_C28AAAAA00360.33 AA00
491zz5_D_C28_A29AAAAA00700.24 AA00
501zz5_D_A29_C30AAAAA08820.28 AA08
511zz5_D_C30_C31AAAAA00930.24 AA00
521zz5_D_C31_A32AAAAA00910.23 AA00
531zz5_D_A32_C33AAwAA01900.23 AA01
541zz5_D_C33_C34AAuAA12430.37 AA12

Steps with non-standard or missing atoms have not been assigned, description of conformers is defined in the table.
Definition of torsion angles
step:
Table of conformers

δ1ε1ζ1α2β2γ2δ2χ1χ2μNNCC
step_torsions
ntC_average
Δ torsions
torsion scores

commentsstep confal = NaN
cartesian RMSD = NaN Å
pseudorotation: NA
details: NA
Similarity of step to class averages

Download

Results as csv or json file.
Best NtC fitted to input structure.

Restraints

Restraints file for REFMAC (steps with RMSD <= 0.5Å)
Commands file for MMB (steps with RMSD <= 0.5Å)
Restraints file for Phenix (steps with RMSD <= 0.5Å) [?]

Definitions

Average parameters (csv), esd values (csv), and Cartesian coordinates of conformers.

Download the papers

Description of DNATCO server:
Černý et al., Nucleic Acids Research, 44, W284 (2016).
Definition of conformers:
Schneider et al., Acta Cryst D, 74, 52-64 (2018).
Example of application:
Schneider et al., Genes, 8(10), 278, (2017).

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